What you need to do is have your settings activity launch in another task. You can do this by specifying its task affinity. This is done with the attribute android:taskAffinity. By default all activities share the same task affinity that defaults to main package specified in the manifest. On your settings activity you can specify android:taskAffinity="your.own.package.SettingsTask" to have the settings activity launch in its own task.
Extra documentation.